Command line: [exonerate -m p2g --showtargetgff -q ./query/SPP00000052_2.0.fa -t ./SPP00000052_2.0.fa/gi|444729247|gb|KB320524.1|/SPP00000052_2.0.fa_gi|444729247|gb|KB320524.1|_genomic.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000052_2.0 # Protein # Phosphoseryl-tRNA kinase  (PSTK) # Human (Homo sapiens)
        Target: gi|444729247|gb|KB320524.1|:subseq(4280000,85000) Tupaia chinensis unplaced genomic scaffold Scaffold000113_1, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1199
   Query range: 1 -> 323
  Target range: 31580 -> 11809

     2 : LysThrAlaGluAsnIleArgGlyThrGlySerAspGlyProArgLysArgGlyLeuCys :    21
         !:! !!|||:!!:!!! ! !!|||.!!|||:!!|||||||||||||||  !|||||||||
         ArgProAlaLysAspThrGlyGlyAlaGlyAlaAspGlyProArgLysLeuGlyLeuCys
 31580 : AGACCCGCAAAGGACACCGGAGGAGCCGGCGCCGACGGCCCGCGGAAGTTAGGACTCTGC : 31523

    22 : ValLeuCysGlyLeuProAlaAlaGlyLysSerThrPheAlaArgAlaLeuAlaHisArg :    41
         |||||||||||||||||||||||||||||||||:!!|||||||||!.!|||::!:!!|||
         ValLeuCysGlyLeuProAlaAlaGlyLysSerSerPheAlaArgValLeuSerAsnArg
 31522 : GTCCTCTGTGGTCTCCCCGCAGCTGGAAAATCTTCCTTTGCTCGCGTCCTCAGCAATCGG : 31463

    42 : LeuGlnGlnGluGlnGlyTrpAlaIleGlyValValAlaTyrAspAspValMetProAsp :    61
         |||!:!||||||  !|||||||||:!!|||||||||||||||||||||||||||||||||
         LeuArgGlnGluIleGlyTrpAlaValGlyValValAlaTyrAspAspValMetProAsp
 31462 : CTGCGGCAAGAGATAGGCTGGGCCGTCGGCGTCGTCGCGTACGATGACGTCATGCCAGAC : 31403

    62 : AlaPheLeuAlaGlyAlaArgAlaArgProAla  >>>> Target Intron 1 >>>> :    73
         |||||||||! !|||:!!!!!|||!:!|||  !           7373 bp         
         AlaPheLeuGluGlySerSerAlaGlnProLeu++                         
 31402 : GCGTTCCTGGAGGGGTCGAGCGCGCAGCCATTGgt......................... : 31365

    74 :   ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuLysTyrLeuGluTyrPheLeuM :    92
           ||||||||||||||||||||||||||||||||||||||||||||||||! !||||||!
         ++ProSerGlnTrpLysLeuLeuArgGlnGluLeuLeuLysTyrLeuGluCysPheLeuI
 31364 : agCCATCCCAGTGGAAATTGCTTCGACAGGAACTGTTGAAGTACCTGGAATGCTTCTTGA : 23937

    93 : etAlaValIleAsnGlyCysGlnMetSerValProProAsnArgThrGluAlaMetTrpG :   112
         !:||||||:!!!!.! !|||:!!||||||!.!|||||||||||||||||||||||||||:
         leAlaValLeuLysAspCysLysMetSerAlaProProAsnArgThrGluAlaMetTrpG
 23936 : TTGCTGTCCTTAAGGACTGTAAGATGTCTGCCCCACCCAACAGGACTGAAGCCATGTGGC : 23877

   113 : luAspPheIleThrCysLeuLysAspGlnAspLeuIlePheSerAlaAlaPheGluAlaG :   132
         !!|||||||||||||||||||||||||||||||||:!!||||||:!!!.!.!!|||  !!
         lnAspPheIleThrCysLeuLysAspGlnAspLeuValPheSerSerValLeuGluAsnP
 23876 : AAGATTTTATAACCTGCTTAAAGGATCAAGATTTGGTATTTTCTTCAGTGCTTGAGAATC : 23817

   133 : lnSerCysTyrLeuLeuThrLysThrAlaValSerArgProLeuPheLeuValLeuAspA :   152
           :!!! !||||||||||||||||||||||||||||||||||||||||||||||||||||
         roAlaSerTyrLeuLeuThrLysThrAlaValSerArgProLeuPheLeuValLeuAspA
 23816 : CCGCTTCCTACCTCTTAACGAAAACTGCTGTTTCCAGACCTTTGTTCTTGGTTTTAGATG : 23757

   153 : spAsnPheTyrTyrGlnSerMetArgTyrGluValTyrGlnLeuAlaArgLys{T}  >> :   170
         |||||||||||||||||||||||||||||||||||||||||||||||||||||{|}    
         spAsnPheTyrTyrGlnSerMetArgTyrGluValTyrGlnLeuAlaArgLys{T}++  
 23756 : ACAATTTTTATTATCAAAGTATGAGATACGAAGTCTACCAACTGGCTCGGAAA{T}gt.. : 23700

   171 : >> Target Intron 2 >>>>  {yr}SerLeuGlyPheCysGlnLeuPheLeuAspC :   181
                 242 bp           {||}|||||||||||||||||||||||||||||||
                                ++{yr}SerLeuGlyPheCysGlnLeuPheLeuAspC
 23699 : .......................ag{AT}TCCTTGGGCTTTTGCCAGCTCTTTTTAGATT : 23428

   182 : ysProLeuGluThrCysLeuGlnArgAsnGlyGlnArgProGlnAlaLeuProProGluT :   201
         |||||||||||.!!|||||||||||||||.!!|||||| !!!:!||||||||| !!||||
         ysProLeuGluAlaCysLeuGlnArgAsnSerGlnArgThrArgAlaLeuProAlaGluT
 23427 : GTCCTCTTGAGGCCTGTTTACAGAGGAACAGCCAGAGAACACGAGCACTACCTGCGGAGA : 23368

   202 : hrIleHisLeuMetGlyArgLysLeuGluLysProAsnProGluLysAsnAlaTrpGluH :   221
         ||||||||||||||! !||||||||||||||||||!:!||||||||||||||||||||||
         hrIleHisLeuMetGluArgLysLeuGluLysProSerProGluLysAsnAlaTrpGluH
 23367 : CCATCCACCTGATGGAAAGGAAGCTAGAAAAGCCCAGCCCTGAAAAGAATGCGTGGGAAC : 23308

   222 : isAsnSerLeuThrIleProSerProAlaCysAlaSerGluAla{Se}  >>>> Targe :   236
         |||||||||||||||||||||||! !.!!! !:!!||||||!.!{||}           1
         isAsnSerLeuThrIleProSerGlnThrTyrSerSerGluVal{Se}++          
 23307 : ACAACAGCCTCACAATTCCAAGTCAAACATATTCTTCGGAGGTC{AG}gt.......... : 23259

   237 : t Intron 3 >>>>  {r}LeuGluValThrAspLeuLeuLeuThrAlaLeuGluAsnP :   250
         0242 bp          {|}||||||||||||!!:|||||||||! !|||||||||||||
                        ++{r}LeuGluValThrGluLeuLeuLeuMetAlaLeuGluAsnP
 23258 : ...............ag{C}CTGGAGGTGACTGAGTTACTGCTCATGGCTTTGGAAAATC : 12979

   251 : roValLysTyrAlaGluAspAsnMetGluGlnLys  >>>> Target Intron 4 >> :   262
         |||||||||||!.!|||||||||!  |||||||||            562 bp       
         roValLysTyrValGluAspAsnThrGluGlnLys++                       
 12978 : CAGTAAAATATGTTGAGGACAATACAGAACAAAAGgt....................... : 12941

   263 : >>  AspThrAspArgIleIleCysSerThrAsnIleLeuHisLysThrAspGlnThrLe :   280
             !!:.!!|||||||||||||||||||||!:!:!!|||||||||.!!|||||||||||
           ++GluAlaAspArgIleIleCysSerThrSerValLeuHisLysAlaAspGlnThrLe
 12940 : ..agGAAGCAGATAGAATTATTTGCTCAACTAGTGTTCTTCATAAAGCTGATCAGACACT : 12327

   281 : uArgArgIleValSerGlnThrMetLysGluAlaLys{G}  >>>> Target Intron :   293
         |||||||||||||||||||||||||||||||||||||{|}            385 bp  
         uArgArgIleValSerGlnThrMetLysGluAlaLys{G}++                  
 12326 : TCGAAGAATTGTATCTCAGACAATGAAGGAGGCAAAA{G}gt.................. : 12285

   294 :  5 >>>>  {ly}AsnGlnGluAlaPheSerGluMet----ThrPheLysGlnArgTrpV :   308
                  {||}||| !!|||!.!|||||||||! !####! !!:!:!!||||||   !
                -+{ly}Asn***GluGlyPheSerGluArg####ArgTyrGluGlnArg---G
 12284 : .......gg{GT}AATTAGGAAGGCTTCTCTGAGAGGAGAGAGATATGAACAAAGG---G : 11857

   309 : alArgAlaAsnHisAlaAlaIleTrpArgIleIleLeuGlyAsnGlu :   323
          ! !!|||||||||||||||:!!||| !!:!!! !  !.!!:::|||
         luGlyAlaAsnHisAlaAlaValTrpTrpValAsnLysSerSerGlu
 11856 : AAGGAGCAAATCATGCTGCTGTCTGGTGGGTCAATAAAAGCTCAGAG : 11810

vulgar: SPP00000052_2.0 1 323 . gi|444729247|gb|KB320524.1|:subseq(4280000,85000) 31580 11809 - 1199 M 71 213 5 0 2 I 0 7369 3 0 2 M 97 291 S 0 1 5 0 2 I 0 238 3 0 2 S 1 2 M 65 195 S 0 2 5 0 2 I 0 10238 3 0 2 S 1 1 M 25 75 5 0 2 I 0 558 3 0 2 M 31 93 S 0 1 5 0 2 I 0 381 3 0 2 S 1 2 M 8 24 F 0 4 M 5 15 G 1 0 M 16 48
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-18
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	gene	11810	31580	1199	-	.	gene_id 1 ; sequence SPP00000052_2.0 ; gene_orientation +
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	cds	31368	31580	.	-	.	
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	exon	31368	31580	.	-	.	insertions 0 ; deletions 0
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice5	31366	31367	.	-	.	intron_id 1 ; splice_site "GT"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	intron	23995	31367	.	-	.	intron_id 1
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice3	23995	23996	.	-	.	intron_id 0 ; splice_site "AG"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	cds	23703	23994	.	-	.	
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	exon	23703	23994	.	-	.	insertions 0 ; deletions 0
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice5	23701	23702	.	-	.	intron_id 2 ; splice_site "GT"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	intron	23461	23702	.	-	.	intron_id 2
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice3	23461	23462	.	-	.	intron_id 1 ; splice_site "AG"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	cds	23262	23460	.	-	.	
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	exon	23262	23460	.	-	.	insertions 0 ; deletions 0
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice5	23260	23261	.	-	.	intron_id 3 ; splice_site "GT"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	intron	13020	23261	.	-	.	intron_id 3
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice3	13020	13021	.	-	.	intron_id 2 ; splice_site "AG"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	cds	12944	13019	.	-	.	
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	exon	12944	13019	.	-	.	insertions 0 ; deletions 0
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice5	12942	12943	.	-	.	intron_id 4 ; splice_site "GT"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	intron	12382	12943	.	-	.	intron_id 4
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice3	12382	12383	.	-	.	intron_id 3 ; splice_site "AG"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	cds	12288	12381	.	-	.	
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	exon	12288	12381	.	-	.	insertions 0 ; deletions 0
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice5	12286	12287	.	-	.	intron_id 5 ; splice_site "GT"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	intron	11903	12287	.	-	.	intron_id 5
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	splice3	11903	11904	.	-	.	intron_id 4 ; splice_site "GG"
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	cds	11810	11902	.	-	.	
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	exon	11810	11902	.	-	.	insertions 0 ; deletions 1 ; frameshifts 4
gi|444729247|gb|KB320524.1|:subseq(4280000,85000)	exonerate:protein2genome:local	similarity	11810	31580	1199	-	.	alignment_id 1 ; Query SPP00000052_2.0 ; Align 31581 2 213 ; Align 23995 73 291 ; Align 23459 171 195 ; Align 13019 237 75 ; Align 12382 262 93 ; Align 11901 294 24 ; Align 11873 302 15 ; Align 11858 308 48
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
